Hello,
Using the defaults and then testing the resulting SAM output seems to
be
what most folks are doing if they do not have access to the original
library construction methods (e.g. size selection). Both SAM Tools
and
Picard are in Galaxy. This is a useful post where the options are
discussed:
http://www.biostars.org/post/show/16556/estimate-insert-size-in-
paired-endmate-pair/
Is the data Illumina? The data source may be able to tell you if the
adapter sequence was actually sequenced and/or if it was removed
already
or not. If present or you just suspect it is present, they would also
have access to the Illumina fasta adapter data. You could also test
with
FastQC (before or after alignment, maybe on just a sample), then
perform
a clip based on those results, and re-run. See the tools in 'NGS: QC
and
manipulation' to perform these tasks.
Going forward, please send questions as a new thread directly to our
mailing list at galaxy-user@bx.psu.edu.
http://wiki.g2.bx.psu.edu/Support#Public_mailing_list_Q_.26_A_discussi
ons
Best,
Jen
Galaxy team
--
Jennifer Jackson
http://galaxyproject.org